First of all, I feel like the second tier special passive skill nodes are too much entangled with each other. Skills like Archion´s Teaching force you to change your character in a specific way. This Skill for example makes you fire two Projectiles that do 40% damage which makes this skill damage-wise only appealing if you choose the right playstyle. In order to make up for the 20% lack in damage your projectiles either must have multihit with a high crit chance or your goal is to spread ailments. So unless you choose one of these two paths this skill is basically worthless.
If you choose spreading ailments as your source of damage, you want to skill Attrition Strategist, Immortal Offering, Insidious Decay and Grievous Affliction. Insidious delay has a penalty on damage that is not damage over time of -30% which forces you to neglect other forms of damage, Indsidious Delay and Archions Teachings especially restrict your character too much; other builds are less appealing which restricts the number of builds you can possibly theorycraft.

Merciless Lethality is another skill that seems not right to me. Usually, in most lategame builds in almost any action-rpg critical damage makes it possible to chip away the enemies health at higher levels and difficulties. For this to be efficient, you need to have high crit chance and crit damage. So if you already go for this setup, picking Merciless Lethality makes your damage shoot through the roof with a 60% crit dmg increase. Its -30% dmg penalty on all non-critical hits on the other hand makes it redundant under a certain threshhold of crit chance. So, if you go for crit chance and crit damage which most endgame do,this skill is a must have. If you don´t, its not with leveling and can make you even weaker.

To conclude, i feel like skills that have a penalty if you don´t play the suggested playstyle just force you too much in a direction, are useless unless when you play the suggested way and are therefore not beneficial for theorycfarfting.